Breadth by Depth: Expanding Our Understanding of the Repair of Transposon-Induced DNA Double Strand Breaks via Deep-Sequencing

DNA Repair (Amst). 2011 Oct 10;10(10):1023-33. doi: 10.1016/j.dnarep.2011.07.011. Epub 2011 Sep 1.


The transposases of DNA transposable elements catalyze the excision of the element from the host genome, but are not involved in the repair of the resulting double-strand break. To elucidate the role of various host DNA repair and damage response proteins in the repair of the hairpin-ended double strand breaks (DSBs) generated during excision of the maize Ac element in Arabidopsis thaliana, we deep-sequenced hundreds of thousands of somatic excision products from a variety of repair- or response-defective mutants. We find that each of these repair/response defects negatively affects the preservation of the ends, resulting in an enhanced frequency of deletions, insertions, and inversions at the excision site. The spectra of the resulting repair products demonstrate, not unexpectedly, that the canonical nonhomologous end joining (NHEJ) proteins DNA ligase IV and KU70 play an important role in the repair of the lesion generated by Ac excision. Our data also indicate that auxiliary NHEJ repair proteins such as DNA ligase VI and DNA polymerase lambda are routinely involved in the repair of these lesions. Roles for the damage response kinases ATM and ATR in the repair of transposition-induced DSBs are also discussed.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • DNA Breaks, Double-Stranded*
  • DNA End-Joining Repair*
  • DNA Ligase ATP
  • DNA Ligases / genetics*
  • DNA Ligases / metabolism
  • DNA Transposable Elements / genetics
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • High-Throughput Nucleotide Sequencing
  • Inverted Repeat Sequences
  • Molecular Sequence Data
  • Sequence Analysis, DNA
  • Zea mays / genetics*
  • Zea mays / metabolism


  • Arabidopsis Proteins
  • DNA Transposable Elements
  • DNA-Binding Proteins
  • KU70 protein, Arabidopsis
  • DNA Ligases
  • DNA Ligase ATP